Multiple sequence alignment - TraesCS5B01G409600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G409600 chr5B 100.000 2561 0 0 1 2561 584868309 584865749 0.000000e+00 4730.0
1 TraesCS5B01G409600 chr5B 96.562 669 23 0 1893 2561 63281543 63282211 0.000000e+00 1109.0
2 TraesCS5B01G409600 chr5B 96.562 669 23 0 1893 2561 362955031 362955699 0.000000e+00 1109.0
3 TraesCS5B01G409600 chr5D 95.105 1573 45 9 268 1829 477297733 477296182 0.000000e+00 2449.0
4 TraesCS5B01G409600 chr5D 94.318 88 5 0 1 88 477297815 477297728 4.440000e-28 135.0
5 TraesCS5B01G409600 chr5A 93.480 1365 70 4 477 1826 596487760 596486400 0.000000e+00 2010.0
6 TraesCS5B01G409600 chr5A 98.851 87 1 0 2 88 596487954 596487868 3.410000e-34 156.0
7 TraesCS5B01G409600 chr2D 96.716 670 22 0 1892 2561 638412816 638413485 0.000000e+00 1116.0
8 TraesCS5B01G409600 chr6D 96.712 669 22 0 1893 2561 432916937 432917605 0.000000e+00 1114.0
9 TraesCS5B01G409600 chr3D 96.712 669 22 0 1893 2561 3363624 3362956 0.000000e+00 1114.0
10 TraesCS5B01G409600 chr3D 95.213 188 8 1 79 266 71527742 71527556 1.930000e-76 296.0
11 TraesCS5B01G409600 chr3D 93.846 195 12 0 83 277 142708586 142708780 6.930000e-76 294.0
12 TraesCS5B01G409600 chr1D 96.712 669 22 0 1893 2561 59877756 59878424 0.000000e+00 1114.0
13 TraesCS5B01G409600 chr1D 92.537 201 13 2 80 280 149049620 149049818 1.160000e-73 287.0
14 TraesCS5B01G409600 chr1B 96.567 670 23 0 1892 2561 14515688 14516357 0.000000e+00 1110.0
15 TraesCS5B01G409600 chrUn 96.562 669 23 0 1893 2561 2002887 2002219 0.000000e+00 1109.0
16 TraesCS5B01G409600 chr6B 96.562 669 23 0 1893 2561 717855103 717855771 0.000000e+00 1109.0
17 TraesCS5B01G409600 chr4D 94.845 194 7 3 75 266 81663633 81663825 1.490000e-77 300.0
18 TraesCS5B01G409600 chr7D 94.330 194 11 0 81 274 161844579 161844386 5.360000e-77 298.0
19 TraesCS5B01G409600 chr7D 93.401 197 11 1 78 272 484321867 484322063 8.960000e-75 291.0
20 TraesCS5B01G409600 chr7D 92.574 202 15 0 83 284 600713511 600713310 8.960000e-75 291.0
21 TraesCS5B01G409600 chr4B 93.939 198 11 1 78 274 429085285 429085482 5.360000e-77 298.0
22 TraesCS5B01G409600 chr2B 95.187 187 9 0 87 273 230774031 230773845 1.930000e-76 296.0
23 TraesCS5B01G409600 chr3A 84.667 150 21 2 1410 1558 534478530 534478678 5.710000e-32 148.0
24 TraesCS5B01G409600 chr3A 100.000 33 0 0 1860 1892 711082328 711082360 7.650000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G409600 chr5B 584865749 584868309 2560 True 4730 4730 100.0000 1 2561 1 chr5B.!!$R1 2560
1 TraesCS5B01G409600 chr5B 63281543 63282211 668 False 1109 1109 96.5620 1893 2561 1 chr5B.!!$F1 668
2 TraesCS5B01G409600 chr5B 362955031 362955699 668 False 1109 1109 96.5620 1893 2561 1 chr5B.!!$F2 668
3 TraesCS5B01G409600 chr5D 477296182 477297815 1633 True 1292 2449 94.7115 1 1829 2 chr5D.!!$R1 1828
4 TraesCS5B01G409600 chr5A 596486400 596487954 1554 True 1083 2010 96.1655 2 1826 2 chr5A.!!$R1 1824
5 TraesCS5B01G409600 chr2D 638412816 638413485 669 False 1116 1116 96.7160 1892 2561 1 chr2D.!!$F1 669
6 TraesCS5B01G409600 chr6D 432916937 432917605 668 False 1114 1114 96.7120 1893 2561 1 chr6D.!!$F1 668
7 TraesCS5B01G409600 chr3D 3362956 3363624 668 True 1114 1114 96.7120 1893 2561 1 chr3D.!!$R1 668
8 TraesCS5B01G409600 chr1D 59877756 59878424 668 False 1114 1114 96.7120 1893 2561 1 chr1D.!!$F1 668
9 TraesCS5B01G409600 chr1B 14515688 14516357 669 False 1110 1110 96.5670 1892 2561 1 chr1B.!!$F1 669
10 TraesCS5B01G409600 chrUn 2002219 2002887 668 True 1109 1109 96.5620 1893 2561 1 chrUn.!!$R1 668
11 TraesCS5B01G409600 chr6B 717855103 717855771 668 False 1109 1109 96.5620 1893 2561 1 chr6B.!!$F1 668

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
102 103 0.184933 CTCAGGGGGTGTTTGGTTCA 59.815 55.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 1857 0.453793 TTTCAAACGGTGCACCACAG 59.546 50.0 34.16 20.92 35.86 3.66 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.190327 TGTTGTTGAACCATCGCATTAGG 59.810 43.478 0.00 0.00 0.00 2.69
89 90 6.923928 GAGATCTCTTTTGAAATCTCAGGG 57.076 41.667 15.80 0.00 46.85 4.45
90 91 5.753716 AGATCTCTTTTGAAATCTCAGGGG 58.246 41.667 0.00 0.00 30.92 4.79
91 92 4.307032 TCTCTTTTGAAATCTCAGGGGG 57.693 45.455 0.00 0.00 31.69 5.40
92 93 3.657727 TCTCTTTTGAAATCTCAGGGGGT 59.342 43.478 0.00 0.00 31.69 4.95
93 94 3.760684 CTCTTTTGAAATCTCAGGGGGTG 59.239 47.826 0.00 0.00 31.69 4.61
94 95 3.140144 TCTTTTGAAATCTCAGGGGGTGT 59.860 43.478 0.00 0.00 31.69 4.16
95 96 3.611025 TTTGAAATCTCAGGGGGTGTT 57.389 42.857 0.00 0.00 31.69 3.32
96 97 3.611025 TTGAAATCTCAGGGGGTGTTT 57.389 42.857 0.00 0.00 31.69 2.83
97 98 2.875296 TGAAATCTCAGGGGGTGTTTG 58.125 47.619 0.00 0.00 0.00 2.93
98 99 2.171003 GAAATCTCAGGGGGTGTTTGG 58.829 52.381 0.00 0.00 0.00 3.28
99 100 1.158007 AATCTCAGGGGGTGTTTGGT 58.842 50.000 0.00 0.00 0.00 3.67
100 101 1.158007 ATCTCAGGGGGTGTTTGGTT 58.842 50.000 0.00 0.00 0.00 3.67
101 102 0.476771 TCTCAGGGGGTGTTTGGTTC 59.523 55.000 0.00 0.00 0.00 3.62
102 103 0.184933 CTCAGGGGGTGTTTGGTTCA 59.815 55.000 0.00 0.00 0.00 3.18
103 104 0.184933 TCAGGGGGTGTTTGGTTCAG 59.815 55.000 0.00 0.00 0.00 3.02
104 105 0.827507 CAGGGGGTGTTTGGTTCAGG 60.828 60.000 0.00 0.00 0.00 3.86
105 106 1.533033 GGGGGTGTTTGGTTCAGGG 60.533 63.158 0.00 0.00 0.00 4.45
106 107 1.539665 GGGGTGTTTGGTTCAGGGA 59.460 57.895 0.00 0.00 0.00 4.20
107 108 0.826256 GGGGTGTTTGGTTCAGGGAC 60.826 60.000 0.00 0.00 0.00 4.46
108 109 0.185175 GGGTGTTTGGTTCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
109 110 1.411074 GGGTGTTTGGTTCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
110 111 2.384828 GGTGTTTGGTTCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
111 112 2.764010 GGTGTTTGGTTCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
112 113 3.196901 GGTGTTTGGTTCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
113 114 4.403113 GGTGTTTGGTTCAGGGACTTTTTA 59.597 41.667 0.00 0.00 34.60 1.52
114 115 5.451381 GGTGTTTGGTTCAGGGACTTTTTAG 60.451 44.000 0.00 0.00 34.60 1.85
115 116 5.126545 GTGTTTGGTTCAGGGACTTTTTAGT 59.873 40.000 0.00 0.00 34.60 2.24
116 117 5.358725 TGTTTGGTTCAGGGACTTTTTAGTC 59.641 40.000 0.00 0.00 34.60 2.59
134 135 3.957591 GTCCCCGAGACTAGAAAAAGT 57.042 47.619 0.00 0.00 42.69 2.66
135 136 3.847542 GTCCCCGAGACTAGAAAAAGTC 58.152 50.000 0.00 0.00 45.20 3.01
148 149 8.905660 ACTAGAAAAAGTCTCTAAAAAGTCCC 57.094 34.615 0.00 0.00 37.84 4.46
149 150 8.715842 ACTAGAAAAAGTCTCTAAAAAGTCCCT 58.284 33.333 0.00 0.00 37.84 4.20
152 153 9.916360 AGAAAAAGTCTCTAAAAAGTCCCTAAA 57.084 29.630 0.00 0.00 0.00 1.85
155 156 8.461249 AAAGTCTCTAAAAAGTCCCTAAAACC 57.539 34.615 0.00 0.00 0.00 3.27
156 157 6.540995 AGTCTCTAAAAAGTCCCTAAAACCC 58.459 40.000 0.00 0.00 0.00 4.11
157 158 6.102174 AGTCTCTAAAAAGTCCCTAAAACCCA 59.898 38.462 0.00 0.00 0.00 4.51
158 159 6.774170 GTCTCTAAAAAGTCCCTAAAACCCAA 59.226 38.462 0.00 0.00 0.00 4.12
159 160 7.286087 GTCTCTAAAAAGTCCCTAAAACCCAAA 59.714 37.037 0.00 0.00 0.00 3.28
160 161 7.286087 TCTCTAAAAAGTCCCTAAAACCCAAAC 59.714 37.037 0.00 0.00 0.00 2.93
161 162 4.659111 AAAAGTCCCTAAAACCCAAACG 57.341 40.909 0.00 0.00 0.00 3.60
162 163 2.281539 AGTCCCTAAAACCCAAACGG 57.718 50.000 0.00 0.00 37.81 4.44
173 174 3.432262 CCAAACGGGAGGGACTTTT 57.568 52.632 0.00 0.00 41.55 2.27
174 175 1.699730 CCAAACGGGAGGGACTTTTT 58.300 50.000 0.00 0.00 41.55 1.94
175 176 1.611977 CCAAACGGGAGGGACTTTTTC 59.388 52.381 0.00 0.00 41.55 2.29
176 177 2.583143 CAAACGGGAGGGACTTTTTCT 58.417 47.619 0.00 0.00 41.55 2.52
177 178 3.497227 CCAAACGGGAGGGACTTTTTCTA 60.497 47.826 0.00 0.00 41.55 2.10
178 179 3.413846 AACGGGAGGGACTTTTTCTAC 57.586 47.619 0.00 0.00 41.55 2.59
179 180 2.332117 ACGGGAGGGACTTTTTCTACA 58.668 47.619 0.00 0.00 41.55 2.74
180 181 2.302157 ACGGGAGGGACTTTTTCTACAG 59.698 50.000 0.00 0.00 41.55 2.74
181 182 2.354805 CGGGAGGGACTTTTTCTACAGG 60.355 54.545 0.00 0.00 41.55 4.00
182 183 2.026169 GGGAGGGACTTTTTCTACAGGG 60.026 54.545 0.00 0.00 41.55 4.45
183 184 2.910977 GGAGGGACTTTTTCTACAGGGA 59.089 50.000 0.00 0.00 41.55 4.20
184 185 3.307550 GGAGGGACTTTTTCTACAGGGAC 60.308 52.174 0.00 0.00 41.55 4.46
185 186 3.583526 GAGGGACTTTTTCTACAGGGACT 59.416 47.826 0.00 0.00 41.55 3.85
186 187 4.759953 AGGGACTTTTTCTACAGGGACTA 58.240 43.478 0.00 0.00 28.08 2.59
187 188 4.778427 AGGGACTTTTTCTACAGGGACTAG 59.222 45.833 0.00 0.00 28.08 2.57
188 189 4.776308 GGGACTTTTTCTACAGGGACTAGA 59.224 45.833 0.00 0.00 36.02 2.43
189 190 5.247792 GGGACTTTTTCTACAGGGACTAGAA 59.752 44.000 0.00 0.00 36.02 2.10
190 191 6.239800 GGGACTTTTTCTACAGGGACTAGAAA 60.240 42.308 0.00 0.00 38.08 2.52
191 192 7.222161 GGACTTTTTCTACAGGGACTAGAAAA 58.778 38.462 0.00 8.58 43.60 2.29
195 196 8.672823 TTTTTCTACAGGGACTAGAAAAAGAC 57.327 34.615 16.61 0.00 46.05 3.01
196 197 7.613551 TTTCTACAGGGACTAGAAAAAGACT 57.386 36.000 0.00 0.00 37.31 3.24
197 198 6.837471 TCTACAGGGACTAGAAAAAGACTC 57.163 41.667 0.00 0.00 36.02 3.36
198 199 6.553857 TCTACAGGGACTAGAAAAAGACTCT 58.446 40.000 0.00 0.00 36.02 3.24
199 200 7.696981 TCTACAGGGACTAGAAAAAGACTCTA 58.303 38.462 0.00 0.00 36.02 2.43
200 201 6.593268 ACAGGGACTAGAAAAAGACTCTAC 57.407 41.667 0.00 0.00 36.02 2.59
201 202 6.316513 ACAGGGACTAGAAAAAGACTCTACT 58.683 40.000 0.00 0.00 36.02 2.57
202 203 6.209788 ACAGGGACTAGAAAAAGACTCTACTG 59.790 42.308 0.00 0.00 36.02 2.74
203 204 5.717654 AGGGACTAGAAAAAGACTCTACTGG 59.282 44.000 0.00 0.00 36.02 4.00
204 205 5.715753 GGGACTAGAAAAAGACTCTACTGGA 59.284 44.000 0.00 0.00 0.00 3.86
205 206 6.127563 GGGACTAGAAAAAGACTCTACTGGAG 60.128 46.154 0.00 0.00 46.87 3.86
206 207 6.660094 GGACTAGAAAAAGACTCTACTGGAGA 59.340 42.308 0.00 0.00 44.45 3.71
243 244 4.635699 TCCCTGGGACTAGAAAAAGTTC 57.364 45.455 12.53 0.00 0.00 3.01
244 245 4.240323 TCCCTGGGACTAGAAAAAGTTCT 58.760 43.478 12.53 0.00 46.18 3.01
245 246 5.408824 TCCCTGGGACTAGAAAAAGTTCTA 58.591 41.667 12.53 0.00 42.53 2.10
258 259 6.993308 AGAAAAAGTTCTAGGACTTCTGAACC 59.007 38.462 16.98 4.21 42.53 3.62
259 260 5.888982 AAAGTTCTAGGACTTCTGAACCA 57.111 39.130 16.98 0.00 38.86 3.67
260 261 5.888982 AAGTTCTAGGACTTCTGAACCAA 57.111 39.130 10.89 0.00 39.45 3.67
261 262 5.888982 AGTTCTAGGACTTCTGAACCAAA 57.111 39.130 0.00 0.00 39.45 3.28
262 263 5.612351 AGTTCTAGGACTTCTGAACCAAAC 58.388 41.667 0.00 2.45 39.45 2.93
263 264 5.130477 AGTTCTAGGACTTCTGAACCAAACA 59.870 40.000 0.00 0.00 39.45 2.83
264 265 4.957296 TCTAGGACTTCTGAACCAAACAC 58.043 43.478 0.58 0.00 0.00 3.32
265 266 2.932261 AGGACTTCTGAACCAAACACC 58.068 47.619 0.58 0.00 0.00 4.16
266 267 2.509964 AGGACTTCTGAACCAAACACCT 59.490 45.455 0.58 0.00 0.00 4.00
267 268 3.053619 AGGACTTCTGAACCAAACACCTT 60.054 43.478 0.58 0.00 0.00 3.50
268 269 3.315470 GGACTTCTGAACCAAACACCTTC 59.685 47.826 0.00 0.00 0.00 3.46
269 270 4.200092 GACTTCTGAACCAAACACCTTCT 58.800 43.478 0.00 0.00 0.00 2.85
270 271 4.600062 ACTTCTGAACCAAACACCTTCTT 58.400 39.130 0.00 0.00 0.00 2.52
324 337 6.238456 CCAAACTTGAAATTTGAAGAAAGCCC 60.238 38.462 22.02 0.00 39.01 5.19
431 444 8.843885 ATACATCATAATGAGTTCACATCCAG 57.156 34.615 0.00 0.00 36.67 3.86
432 445 6.892485 ACATCATAATGAGTTCACATCCAGA 58.108 36.000 0.00 0.00 36.67 3.86
462 475 2.157668 CACTGAACCTGTAACGACATGC 59.842 50.000 0.00 0.00 34.24 4.06
473 486 1.448985 ACGACATGCACATAACCCAC 58.551 50.000 0.00 0.00 0.00 4.61
474 487 1.271108 ACGACATGCACATAACCCACA 60.271 47.619 0.00 0.00 0.00 4.17
475 488 1.809547 CGACATGCACATAACCCACAA 59.190 47.619 0.00 0.00 0.00 3.33
476 489 2.414029 CGACATGCACATAACCCACAAC 60.414 50.000 0.00 0.00 0.00 3.32
477 490 1.892474 ACATGCACATAACCCACAACC 59.108 47.619 0.00 0.00 0.00 3.77
478 491 1.891811 CATGCACATAACCCACAACCA 59.108 47.619 0.00 0.00 0.00 3.67
479 492 1.323412 TGCACATAACCCACAACCAC 58.677 50.000 0.00 0.00 0.00 4.16
504 517 4.330074 AGTTTCCAGTATTCGAAATCTGCG 59.670 41.667 20.29 15.46 31.10 5.18
619 632 1.548269 CTCAGTGGAAGGTGTCTCTCC 59.452 57.143 0.00 0.00 0.00 3.71
641 654 0.233332 GTTGTCAGTCGCTGAACTGC 59.767 55.000 10.46 1.59 45.12 4.40
656 669 1.797025 ACTGCGGAGAAGCACTAAAC 58.203 50.000 12.26 0.00 42.92 2.01
734 747 1.519234 GCGAGCCATGTGATCACGA 60.519 57.895 20.54 10.47 0.00 4.35
740 753 0.464193 CCATGTGATCACGATGCCCA 60.464 55.000 20.54 1.80 0.00 5.36
794 807 2.872028 GCAGTTGCCAACGAACTTG 58.128 52.632 1.20 0.00 36.23 3.16
822 835 3.636043 CGGTCAAACGCACACGCT 61.636 61.111 0.00 0.00 45.53 5.07
831 844 2.813179 CGCACACGCTAAGATGGCC 61.813 63.158 0.00 0.00 35.30 5.36
945 967 3.852286 CATTGGCATTGCACAAGTGTAT 58.148 40.909 11.39 0.00 0.00 2.29
948 970 4.333913 TGGCATTGCACAAGTGTATTTT 57.666 36.364 11.39 0.00 0.00 1.82
971 993 4.251543 TCAGTGATCTTGTAGCGTTTGA 57.748 40.909 0.00 0.00 0.00 2.69
1230 1252 3.849951 GGGAAGATCTCCGGCGCA 61.850 66.667 10.83 0.00 46.51 6.09
1380 1402 3.069778 GACCTGAGGAGGGCGTTT 58.930 61.111 4.99 0.00 44.84 3.60
1401 1423 1.964373 GGTGTTCAACGCCGTGGAT 60.964 57.895 3.86 0.00 39.19 3.41
1644 1666 0.034476 GATGAGCCCATGCAGATCGA 59.966 55.000 0.00 0.00 41.13 3.59
1646 1668 0.250166 TGAGCCCATGCAGATCGATG 60.250 55.000 0.54 0.00 41.13 3.84
1703 1725 6.163476 GTCTCACAAGTGACACCAATGTATA 58.837 40.000 0.84 0.00 39.95 1.47
1826 1857 6.136541 AGTGAGAAGTTCCATGAACAAAAC 57.863 37.500 9.42 1.45 44.11 2.43
1827 1858 5.888161 AGTGAGAAGTTCCATGAACAAAACT 59.112 36.000 9.42 3.37 44.11 2.66
1828 1859 5.973565 GTGAGAAGTTCCATGAACAAAACTG 59.026 40.000 9.42 0.00 44.11 3.16
1829 1860 5.652014 TGAGAAGTTCCATGAACAAAACTGT 59.348 36.000 9.42 0.00 44.11 3.55
1830 1861 5.894807 AGAAGTTCCATGAACAAAACTGTG 58.105 37.500 9.42 0.00 44.11 3.66
1831 1862 4.654091 AGTTCCATGAACAAAACTGTGG 57.346 40.909 9.42 0.00 44.11 4.17
1832 1863 4.023291 AGTTCCATGAACAAAACTGTGGT 58.977 39.130 9.42 0.00 44.11 4.16
1833 1864 4.111916 GTTCCATGAACAAAACTGTGGTG 58.888 43.478 0.00 0.00 41.62 4.17
1834 1865 2.100584 TCCATGAACAAAACTGTGGTGC 59.899 45.455 0.00 0.00 0.00 5.01
1835 1866 2.159128 CCATGAACAAAACTGTGGTGCA 60.159 45.455 0.00 0.00 0.00 4.57
1836 1867 2.645730 TGAACAAAACTGTGGTGCAC 57.354 45.000 8.80 8.80 34.56 4.57
1837 1868 1.203523 TGAACAAAACTGTGGTGCACC 59.796 47.619 29.67 29.67 32.73 5.01
1838 1869 0.172352 AACAAAACTGTGGTGCACCG 59.828 50.000 30.07 18.69 39.43 4.94
1839 1870 0.963355 ACAAAACTGTGGTGCACCGT 60.963 50.000 30.07 19.38 39.43 4.83
1840 1871 0.172352 CAAAACTGTGGTGCACCGTT 59.828 50.000 30.07 23.78 41.96 4.44
1841 1872 2.573920 AAACTGTGGTGCACCGTTT 58.426 47.368 30.07 27.51 43.27 3.60
1842 1873 0.172352 AAACTGTGGTGCACCGTTTG 59.828 50.000 28.64 21.62 45.13 2.93
1843 1874 0.678366 AACTGTGGTGCACCGTTTGA 60.678 50.000 30.07 10.28 38.30 2.69
1844 1875 0.678366 ACTGTGGTGCACCGTTTGAA 60.678 50.000 30.07 9.47 39.43 2.69
1845 1876 0.453793 CTGTGGTGCACCGTTTGAAA 59.546 50.000 30.07 8.66 39.43 2.69
1846 1877 1.066908 CTGTGGTGCACCGTTTGAAAT 59.933 47.619 30.07 0.00 39.43 2.17
1847 1878 1.478510 TGTGGTGCACCGTTTGAAATT 59.521 42.857 30.07 0.00 39.43 1.82
1848 1879 2.093973 TGTGGTGCACCGTTTGAAATTT 60.094 40.909 30.07 0.00 39.43 1.82
1849 1880 2.933260 GTGGTGCACCGTTTGAAATTTT 59.067 40.909 30.07 0.00 39.43 1.82
1850 1881 4.113354 GTGGTGCACCGTTTGAAATTTTA 58.887 39.130 30.07 5.45 39.43 1.52
1851 1882 4.208253 GTGGTGCACCGTTTGAAATTTTAG 59.792 41.667 30.07 0.00 39.43 1.85
1852 1883 3.738791 GGTGCACCGTTTGAAATTTTAGG 59.261 43.478 22.49 0.00 0.00 2.69
1853 1884 3.183574 GTGCACCGTTTGAAATTTTAGGC 59.816 43.478 5.22 0.00 0.00 3.93
1854 1885 2.734606 GCACCGTTTGAAATTTTAGGCC 59.265 45.455 0.00 0.00 0.00 5.19
1855 1886 3.554129 GCACCGTTTGAAATTTTAGGCCT 60.554 43.478 11.78 11.78 0.00 5.19
1856 1887 4.234574 CACCGTTTGAAATTTTAGGCCTC 58.765 43.478 9.68 0.00 0.00 4.70
1857 1888 3.257375 ACCGTTTGAAATTTTAGGCCTCC 59.743 43.478 9.68 0.00 0.00 4.30
1858 1889 3.509967 CCGTTTGAAATTTTAGGCCTCCT 59.490 43.478 9.68 0.00 37.71 3.69
1859 1890 4.021456 CCGTTTGAAATTTTAGGCCTCCTT 60.021 41.667 9.68 0.00 34.61 3.36
1860 1891 5.510690 CCGTTTGAAATTTTAGGCCTCCTTT 60.511 40.000 9.68 4.88 34.61 3.11
1861 1892 5.633601 CGTTTGAAATTTTAGGCCTCCTTTC 59.366 40.000 9.68 14.57 34.61 2.62
1862 1893 6.521162 GTTTGAAATTTTAGGCCTCCTTTCA 58.479 36.000 9.68 16.96 34.61 2.69
1863 1894 6.933514 TTGAAATTTTAGGCCTCCTTTCAT 57.066 33.333 22.32 4.26 34.61 2.57
1864 1895 8.311109 GTTTGAAATTTTAGGCCTCCTTTCATA 58.689 33.333 22.32 17.79 34.61 2.15
1865 1896 7.645058 TGAAATTTTAGGCCTCCTTTCATAG 57.355 36.000 9.68 0.00 34.61 2.23
1866 1897 6.607198 TGAAATTTTAGGCCTCCTTTCATAGG 59.393 38.462 9.68 0.00 46.27 2.57
1867 1898 4.519906 TTTTAGGCCTCCTTTCATAGGG 57.480 45.455 9.68 0.00 44.86 3.53
1868 1899 2.889522 TAGGCCTCCTTTCATAGGGT 57.110 50.000 9.68 0.00 44.86 4.34
1869 1900 1.987080 AGGCCTCCTTTCATAGGGTT 58.013 50.000 0.00 0.00 44.86 4.11
1870 1901 1.566231 AGGCCTCCTTTCATAGGGTTG 59.434 52.381 0.00 0.00 44.86 3.77
1871 1902 1.410224 GGCCTCCTTTCATAGGGTTGG 60.410 57.143 0.00 0.00 44.86 3.77
1872 1903 1.410224 GCCTCCTTTCATAGGGTTGGG 60.410 57.143 0.00 0.00 44.86 4.12
1873 1904 2.205342 CCTCCTTTCATAGGGTTGGGA 58.795 52.381 0.00 0.00 44.86 4.37
1874 1905 2.580783 CCTCCTTTCATAGGGTTGGGAA 59.419 50.000 0.00 0.00 44.86 3.97
1875 1906 3.011257 CCTCCTTTCATAGGGTTGGGAAA 59.989 47.826 0.00 0.00 44.86 3.13
1876 1907 4.326132 CCTCCTTTCATAGGGTTGGGAAAT 60.326 45.833 0.00 0.00 44.86 2.17
1877 1908 4.867086 TCCTTTCATAGGGTTGGGAAATC 58.133 43.478 0.00 0.00 44.86 2.17
1878 1909 4.293634 TCCTTTCATAGGGTTGGGAAATCA 59.706 41.667 0.00 0.00 44.86 2.57
1879 1910 5.043432 TCCTTTCATAGGGTTGGGAAATCAT 60.043 40.000 0.00 0.00 44.86 2.45
1880 1911 6.161348 TCCTTTCATAGGGTTGGGAAATCATA 59.839 38.462 0.00 0.00 44.86 2.15
1881 1912 6.491403 CCTTTCATAGGGTTGGGAAATCATAG 59.509 42.308 0.00 0.00 40.67 2.23
1882 1913 5.582950 TCATAGGGTTGGGAAATCATAGG 57.417 43.478 0.00 0.00 0.00 2.57
1883 1914 5.231552 TCATAGGGTTGGGAAATCATAGGA 58.768 41.667 0.00 0.00 0.00 2.94
1884 1915 5.674496 TCATAGGGTTGGGAAATCATAGGAA 59.326 40.000 0.00 0.00 0.00 3.36
1885 1916 6.335311 TCATAGGGTTGGGAAATCATAGGAAT 59.665 38.462 0.00 0.00 0.00 3.01
1886 1917 7.519355 TCATAGGGTTGGGAAATCATAGGAATA 59.481 37.037 0.00 0.00 0.00 1.75
1887 1918 6.206180 AGGGTTGGGAAATCATAGGAATAG 57.794 41.667 0.00 0.00 0.00 1.73
1888 1919 5.917087 AGGGTTGGGAAATCATAGGAATAGA 59.083 40.000 0.00 0.00 0.00 1.98
1889 1920 6.392842 AGGGTTGGGAAATCATAGGAATAGAA 59.607 38.462 0.00 0.00 0.00 2.10
1890 1921 7.066781 GGGTTGGGAAATCATAGGAATAGAAA 58.933 38.462 0.00 0.00 0.00 2.52
1909 1940 3.350219 AAACGCATTCTGAGGTACCAT 57.650 42.857 15.94 0.00 0.00 3.55
2017 2048 1.531149 CAAAAGACAACCTCGCACGAT 59.469 47.619 0.00 0.00 0.00 3.73
2050 2081 5.295045 TCGGGAAGTAAGAAGTGTTGTTTTC 59.705 40.000 0.00 0.00 0.00 2.29
2320 2351 3.187022 GCAGGTTATTTTCCGTTGTACGT 59.813 43.478 0.00 0.00 40.58 3.57
2330 2361 1.400113 CCGTTGTACGTACTCGCTTCA 60.400 52.381 25.12 1.43 40.58 3.02
2342 2373 2.426024 ACTCGCTTCATACGTGGTGTAT 59.574 45.455 0.00 0.00 44.73 2.29
2445 2476 3.840991 ACATGGATGGCAGCATAATCTT 58.159 40.909 4.64 0.00 0.00 2.40
2452 2483 1.586422 GCAGCATAATCTTCGGCTCA 58.414 50.000 0.00 0.00 33.60 4.26
2557 2588 5.818678 TTATCAGACTACTGGTGTTTGGT 57.181 39.130 0.00 0.00 43.60 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 2.954989 GGGAGCAGGGAAATCTGAAATC 59.045 50.000 0.00 0.00 36.93 2.17
86 87 1.541672 CCTGAACCAAACACCCCCT 59.458 57.895 0.00 0.00 0.00 4.79
87 88 1.533033 CCCTGAACCAAACACCCCC 60.533 63.158 0.00 0.00 0.00 5.40
88 89 0.826256 GTCCCTGAACCAAACACCCC 60.826 60.000 0.00 0.00 0.00 4.95
89 90 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61
90 91 2.067365 AAGTCCCTGAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
91 92 4.465632 AAAAAGTCCCTGAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
92 93 5.265989 ACTAAAAAGTCCCTGAACCAAACA 58.734 37.500 0.00 0.00 0.00 2.83
93 94 5.828747 GACTAAAAAGTCCCTGAACCAAAC 58.171 41.667 0.00 0.00 32.97 2.93
114 115 3.847542 GACTTTTTCTAGTCTCGGGGAC 58.152 50.000 0.00 0.00 44.80 4.46
122 123 8.991026 GGGACTTTTTAGAGACTTTTTCTAGTC 58.009 37.037 0.00 0.00 43.90 2.59
123 124 8.715842 AGGGACTTTTTAGAGACTTTTTCTAGT 58.284 33.333 0.00 0.00 28.84 2.57
126 127 9.916360 TTTAGGGACTTTTTAGAGACTTTTTCT 57.084 29.630 0.00 0.00 41.75 2.52
129 130 8.910944 GGTTTTAGGGACTTTTTAGAGACTTTT 58.089 33.333 0.00 0.00 41.75 2.27
130 131 7.504911 GGGTTTTAGGGACTTTTTAGAGACTTT 59.495 37.037 0.00 0.00 41.75 2.66
131 132 7.002879 GGGTTTTAGGGACTTTTTAGAGACTT 58.997 38.462 0.00 0.00 41.75 3.01
132 133 6.102174 TGGGTTTTAGGGACTTTTTAGAGACT 59.898 38.462 0.00 0.00 41.75 3.24
133 134 6.301486 TGGGTTTTAGGGACTTTTTAGAGAC 58.699 40.000 0.00 0.00 41.75 3.36
134 135 6.518516 TGGGTTTTAGGGACTTTTTAGAGA 57.481 37.500 0.00 0.00 41.75 3.10
135 136 7.431249 GTTTGGGTTTTAGGGACTTTTTAGAG 58.569 38.462 0.00 0.00 41.75 2.43
136 137 6.039605 CGTTTGGGTTTTAGGGACTTTTTAGA 59.960 38.462 0.00 0.00 41.75 2.10
137 138 6.210796 CGTTTGGGTTTTAGGGACTTTTTAG 58.789 40.000 0.00 0.00 41.75 1.85
138 139 5.068855 CCGTTTGGGTTTTAGGGACTTTTTA 59.931 40.000 0.00 0.00 41.75 1.52
139 140 4.141892 CCGTTTGGGTTTTAGGGACTTTTT 60.142 41.667 0.00 0.00 41.75 1.94
140 141 3.385433 CCGTTTGGGTTTTAGGGACTTTT 59.615 43.478 0.00 0.00 41.75 2.27
141 142 2.960384 CCGTTTGGGTTTTAGGGACTTT 59.040 45.455 0.00 0.00 41.75 2.66
142 143 2.589720 CCGTTTGGGTTTTAGGGACTT 58.410 47.619 0.00 0.00 41.75 3.01
143 144 2.281539 CCGTTTGGGTTTTAGGGACT 57.718 50.000 0.00 0.00 46.37 3.85
155 156 1.611977 GAAAAAGTCCCTCCCGTTTGG 59.388 52.381 0.00 0.00 0.00 3.28
156 157 2.583143 AGAAAAAGTCCCTCCCGTTTG 58.417 47.619 0.00 0.00 0.00 2.93
157 158 3.136992 TGTAGAAAAAGTCCCTCCCGTTT 59.863 43.478 0.00 0.00 0.00 3.60
158 159 2.707257 TGTAGAAAAAGTCCCTCCCGTT 59.293 45.455 0.00 0.00 0.00 4.44
159 160 2.302157 CTGTAGAAAAAGTCCCTCCCGT 59.698 50.000 0.00 0.00 0.00 5.28
160 161 2.354805 CCTGTAGAAAAAGTCCCTCCCG 60.355 54.545 0.00 0.00 0.00 5.14
161 162 2.026169 CCCTGTAGAAAAAGTCCCTCCC 60.026 54.545 0.00 0.00 0.00 4.30
162 163 2.910977 TCCCTGTAGAAAAAGTCCCTCC 59.089 50.000 0.00 0.00 0.00 4.30
163 164 3.583526 AGTCCCTGTAGAAAAAGTCCCTC 59.416 47.826 0.00 0.00 0.00 4.30
164 165 3.599348 AGTCCCTGTAGAAAAAGTCCCT 58.401 45.455 0.00 0.00 0.00 4.20
165 166 4.776308 TCTAGTCCCTGTAGAAAAAGTCCC 59.224 45.833 0.00 0.00 0.00 4.46
166 167 5.997384 TCTAGTCCCTGTAGAAAAAGTCC 57.003 43.478 0.00 0.00 0.00 3.85
172 173 7.509659 AGAGTCTTTTTCTAGTCCCTGTAGAAA 59.490 37.037 1.96 1.96 42.24 2.52
173 174 7.011382 AGAGTCTTTTTCTAGTCCCTGTAGAA 58.989 38.462 0.00 0.00 35.21 2.10
174 175 6.553857 AGAGTCTTTTTCTAGTCCCTGTAGA 58.446 40.000 0.00 0.00 0.00 2.59
175 176 6.844097 AGAGTCTTTTTCTAGTCCCTGTAG 57.156 41.667 0.00 0.00 0.00 2.74
176 177 7.393796 CAGTAGAGTCTTTTTCTAGTCCCTGTA 59.606 40.741 0.00 0.00 30.30 2.74
177 178 6.209788 CAGTAGAGTCTTTTTCTAGTCCCTGT 59.790 42.308 0.00 0.00 30.30 4.00
178 179 6.350612 CCAGTAGAGTCTTTTTCTAGTCCCTG 60.351 46.154 0.00 0.00 30.30 4.45
179 180 5.717654 CCAGTAGAGTCTTTTTCTAGTCCCT 59.282 44.000 0.00 0.00 30.30 4.20
180 181 5.715753 TCCAGTAGAGTCTTTTTCTAGTCCC 59.284 44.000 0.00 0.00 30.30 4.46
181 182 6.660094 TCTCCAGTAGAGTCTTTTTCTAGTCC 59.340 42.308 0.00 0.00 43.71 3.85
182 183 7.690952 TCTCCAGTAGAGTCTTTTTCTAGTC 57.309 40.000 0.00 0.00 43.71 2.59
183 184 7.696992 CTCTCCAGTAGAGTCTTTTTCTAGT 57.303 40.000 0.00 0.00 45.85 2.57
221 222 4.041815 AGAACTTTTTCTAGTCCCAGGGAC 59.958 45.833 29.64 29.64 42.50 4.46
222 223 4.240323 AGAACTTTTTCTAGTCCCAGGGA 58.760 43.478 3.01 3.01 40.54 4.20
223 224 4.642466 AGAACTTTTTCTAGTCCCAGGG 57.358 45.455 0.00 0.00 40.54 4.45
232 233 8.148999 GGTTCAGAAGTCCTAGAACTTTTTCTA 58.851 37.037 0.00 0.00 42.44 2.10
233 234 6.993308 GGTTCAGAAGTCCTAGAACTTTTTCT 59.007 38.462 0.00 0.00 44.70 2.52
234 235 6.766467 TGGTTCAGAAGTCCTAGAACTTTTTC 59.234 38.462 0.00 0.00 39.55 2.29
235 236 6.659824 TGGTTCAGAAGTCCTAGAACTTTTT 58.340 36.000 0.00 0.00 39.55 1.94
236 237 6.248569 TGGTTCAGAAGTCCTAGAACTTTT 57.751 37.500 0.00 0.00 39.55 2.27
237 238 5.888982 TGGTTCAGAAGTCCTAGAACTTT 57.111 39.130 0.00 0.00 39.55 2.66
238 239 5.888982 TTGGTTCAGAAGTCCTAGAACTT 57.111 39.130 0.00 0.00 42.10 2.66
239 240 5.130477 TGTTTGGTTCAGAAGTCCTAGAACT 59.870 40.000 0.00 0.00 40.05 3.01
240 241 5.236695 GTGTTTGGTTCAGAAGTCCTAGAAC 59.763 44.000 0.00 0.00 39.59 3.01
241 242 5.365619 GTGTTTGGTTCAGAAGTCCTAGAA 58.634 41.667 0.00 0.00 0.00 2.10
242 243 4.202326 GGTGTTTGGTTCAGAAGTCCTAGA 60.202 45.833 0.00 0.00 0.00 2.43
243 244 4.065789 GGTGTTTGGTTCAGAAGTCCTAG 58.934 47.826 0.00 0.00 0.00 3.02
244 245 3.714798 AGGTGTTTGGTTCAGAAGTCCTA 59.285 43.478 0.00 0.00 0.00 2.94
245 246 2.509964 AGGTGTTTGGTTCAGAAGTCCT 59.490 45.455 0.00 0.00 0.00 3.85
246 247 2.932261 AGGTGTTTGGTTCAGAAGTCC 58.068 47.619 0.00 0.00 0.00 3.85
247 248 4.200092 AGAAGGTGTTTGGTTCAGAAGTC 58.800 43.478 0.00 0.00 0.00 3.01
248 249 4.236527 AGAAGGTGTTTGGTTCAGAAGT 57.763 40.909 0.00 0.00 0.00 3.01
249 250 5.823045 ACTAAGAAGGTGTTTGGTTCAGAAG 59.177 40.000 0.00 0.00 0.00 2.85
250 251 5.751586 ACTAAGAAGGTGTTTGGTTCAGAA 58.248 37.500 0.00 0.00 0.00 3.02
251 252 5.367945 ACTAAGAAGGTGTTTGGTTCAGA 57.632 39.130 0.00 0.00 0.00 3.27
252 253 6.371825 GGATACTAAGAAGGTGTTTGGTTCAG 59.628 42.308 0.00 0.00 0.00 3.02
253 254 6.183361 TGGATACTAAGAAGGTGTTTGGTTCA 60.183 38.462 0.00 0.00 37.61 3.18
254 255 6.235664 TGGATACTAAGAAGGTGTTTGGTTC 58.764 40.000 0.00 0.00 37.61 3.62
255 256 6.195600 TGGATACTAAGAAGGTGTTTGGTT 57.804 37.500 0.00 0.00 37.61 3.67
256 257 5.836024 TGGATACTAAGAAGGTGTTTGGT 57.164 39.130 0.00 0.00 37.61 3.67
257 258 6.653989 AGATGGATACTAAGAAGGTGTTTGG 58.346 40.000 0.00 0.00 37.61 3.28
258 259 8.043710 AGAAGATGGATACTAAGAAGGTGTTTG 58.956 37.037 0.00 0.00 37.61 2.93
259 260 8.152023 AGAAGATGGATACTAAGAAGGTGTTT 57.848 34.615 0.00 0.00 37.61 2.83
260 261 7.741554 AGAAGATGGATACTAAGAAGGTGTT 57.258 36.000 0.00 0.00 37.61 3.32
261 262 7.621683 AGAAGAAGATGGATACTAAGAAGGTGT 59.378 37.037 0.00 0.00 37.61 4.16
262 263 8.017418 AGAAGAAGATGGATACTAAGAAGGTG 57.983 38.462 0.00 0.00 37.61 4.00
263 264 8.616799 AAGAAGAAGATGGATACTAAGAAGGT 57.383 34.615 0.00 0.00 37.61 3.50
264 265 9.898152 AAAAGAAGAAGATGGATACTAAGAAGG 57.102 33.333 0.00 0.00 37.61 3.46
324 337 2.492088 TCACAGTAGTGGTTCCTGATCG 59.508 50.000 1.92 0.00 45.91 3.69
431 444 7.012138 TCGTTACAGGTTCAGTGATAGTATCTC 59.988 40.741 11.40 7.80 0.00 2.75
432 445 6.827251 TCGTTACAGGTTCAGTGATAGTATCT 59.173 38.462 11.40 0.00 0.00 1.98
462 475 2.955660 ACTTGTGGTTGTGGGTTATGTG 59.044 45.455 0.00 0.00 0.00 3.21
473 486 4.513692 TCGAATACTGGAAACTTGTGGTTG 59.486 41.667 0.00 0.00 38.29 3.77
474 487 4.710324 TCGAATACTGGAAACTTGTGGTT 58.290 39.130 0.00 0.00 40.28 3.67
475 488 4.345859 TCGAATACTGGAAACTTGTGGT 57.654 40.909 0.00 0.00 0.00 4.16
476 489 5.682943 TTTCGAATACTGGAAACTTGTGG 57.317 39.130 0.00 0.00 0.00 4.17
477 490 7.017645 CAGATTTCGAATACTGGAAACTTGTG 58.982 38.462 18.27 0.00 35.21 3.33
478 491 6.348540 GCAGATTTCGAATACTGGAAACTTGT 60.349 38.462 23.58 0.00 35.21 3.16
479 492 6.024049 GCAGATTTCGAATACTGGAAACTTG 58.976 40.000 23.58 6.73 35.21 3.16
504 517 2.227388 TCTTTCACGAGGTTAGGACGAC 59.773 50.000 0.00 0.00 0.00 4.34
577 590 6.018589 AGAATTTTAACTCTTGGCAGCTTC 57.981 37.500 0.00 0.00 0.00 3.86
580 593 5.048434 ACTGAGAATTTTAACTCTTGGCAGC 60.048 40.000 0.00 0.00 34.65 5.25
619 632 0.861837 GTTCAGCGACTGACAACTGG 59.138 55.000 8.73 0.00 40.46 4.00
641 654 3.927142 CCTACTTGTTTAGTGCTTCTCCG 59.073 47.826 0.00 0.00 37.73 4.63
656 669 1.517257 CGAGACAGCGCCCTACTTG 60.517 63.158 2.29 0.00 0.00 3.16
740 753 1.366319 ACTGTCAGCTTCTCCCCATT 58.634 50.000 0.00 0.00 0.00 3.16
749 762 3.450457 CCTTCCTGAGATACTGTCAGCTT 59.550 47.826 0.00 0.00 40.22 3.74
794 807 1.393539 CGTTTGACCGGTCATGATGAC 59.606 52.381 36.52 25.25 46.23 3.06
820 833 1.596477 CAGGAGCGGCCATCTTAGC 60.596 63.158 2.24 0.00 40.02 3.09
822 835 1.909459 TTGCAGGAGCGGCCATCTTA 61.909 55.000 2.24 0.00 46.23 2.10
948 970 5.053811 TCAAACGCTACAAGATCACTGAAA 58.946 37.500 0.00 0.00 0.00 2.69
961 983 2.153247 CGTCACAACTCTCAAACGCTAC 59.847 50.000 0.00 0.00 0.00 3.58
965 987 2.150611 CGTACGTCACAACTCTCAAACG 59.849 50.000 7.22 0.00 36.29 3.60
971 993 1.602165 CCTTGCGTACGTCACAACTCT 60.602 52.381 17.90 0.00 0.00 3.24
1039 1061 3.808656 GAAGCTGCTCTTGCCCGC 61.809 66.667 1.00 0.00 38.71 6.13
1380 1402 1.885388 CACGGCGTTGAACACCTCA 60.885 57.895 11.19 0.00 0.00 3.86
1744 1766 6.610741 AAAAACACAGTCTTCTCTAAGCAG 57.389 37.500 0.00 0.00 32.36 4.24
1775 1799 3.132646 ACAGCCATTTTGCAGAGTTGAAA 59.867 39.130 0.00 0.00 0.00 2.69
1780 1804 2.821969 CCTTACAGCCATTTTGCAGAGT 59.178 45.455 0.00 0.00 0.00 3.24
1826 1857 0.453793 TTTCAAACGGTGCACCACAG 59.546 50.000 34.16 20.92 35.86 3.66
1827 1858 1.107114 ATTTCAAACGGTGCACCACA 58.893 45.000 34.16 9.10 35.86 4.17
1828 1859 2.217429 AATTTCAAACGGTGCACCAC 57.783 45.000 34.16 9.94 35.14 4.16
1829 1860 2.969628 AAATTTCAAACGGTGCACCA 57.030 40.000 34.16 14.49 35.14 4.17
1830 1861 3.738791 CCTAAAATTTCAAACGGTGCACC 59.261 43.478 26.78 26.78 0.00 5.01
1831 1862 3.183574 GCCTAAAATTTCAAACGGTGCAC 59.816 43.478 8.80 8.80 0.00 4.57
1832 1863 3.385577 GCCTAAAATTTCAAACGGTGCA 58.614 40.909 0.00 0.00 0.00 4.57
1833 1864 2.734606 GGCCTAAAATTTCAAACGGTGC 59.265 45.455 0.00 0.00 0.00 5.01
1834 1865 4.234574 GAGGCCTAAAATTTCAAACGGTG 58.765 43.478 4.42 0.00 0.00 4.94
1835 1866 3.257375 GGAGGCCTAAAATTTCAAACGGT 59.743 43.478 4.42 0.00 0.00 4.83
1836 1867 3.509967 AGGAGGCCTAAAATTTCAAACGG 59.490 43.478 4.42 0.00 28.47 4.44
1837 1868 4.783764 AGGAGGCCTAAAATTTCAAACG 57.216 40.909 4.42 0.00 28.47 3.60
1838 1869 6.521162 TGAAAGGAGGCCTAAAATTTCAAAC 58.479 36.000 22.25 2.28 34.66 2.93
1839 1870 6.739331 TGAAAGGAGGCCTAAAATTTCAAA 57.261 33.333 22.25 8.54 34.66 2.69
1840 1871 6.933514 ATGAAAGGAGGCCTAAAATTTCAA 57.066 33.333 25.57 15.65 39.34 2.69
1841 1872 7.645058 CTATGAAAGGAGGCCTAAAATTTCA 57.355 36.000 24.70 24.70 39.96 2.69
1856 1887 4.609301 TGATTTCCCAACCCTATGAAAGG 58.391 43.478 0.00 0.00 46.09 3.11
1857 1888 6.491403 CCTATGATTTCCCAACCCTATGAAAG 59.509 42.308 0.00 0.00 30.96 2.62
1858 1889 6.161348 TCCTATGATTTCCCAACCCTATGAAA 59.839 38.462 0.00 0.00 0.00 2.69
1859 1890 5.674496 TCCTATGATTTCCCAACCCTATGAA 59.326 40.000 0.00 0.00 0.00 2.57
1860 1891 5.231552 TCCTATGATTTCCCAACCCTATGA 58.768 41.667 0.00 0.00 0.00 2.15
1861 1892 5.582950 TCCTATGATTTCCCAACCCTATG 57.417 43.478 0.00 0.00 0.00 2.23
1862 1893 6.803587 ATTCCTATGATTTCCCAACCCTAT 57.196 37.500 0.00 0.00 0.00 2.57
1863 1894 7.086260 TCTATTCCTATGATTTCCCAACCCTA 58.914 38.462 0.00 0.00 0.00 3.53
1864 1895 5.917087 TCTATTCCTATGATTTCCCAACCCT 59.083 40.000 0.00 0.00 0.00 4.34
1865 1896 6.200878 TCTATTCCTATGATTTCCCAACCC 57.799 41.667 0.00 0.00 0.00 4.11
1866 1897 8.414003 GTTTTCTATTCCTATGATTTCCCAACC 58.586 37.037 0.00 0.00 0.00 3.77
1867 1898 8.129211 CGTTTTCTATTCCTATGATTTCCCAAC 58.871 37.037 0.00 0.00 0.00 3.77
1868 1899 7.201785 GCGTTTTCTATTCCTATGATTTCCCAA 60.202 37.037 0.00 0.00 0.00 4.12
1869 1900 6.262273 GCGTTTTCTATTCCTATGATTTCCCA 59.738 38.462 0.00 0.00 0.00 4.37
1870 1901 6.262273 TGCGTTTTCTATTCCTATGATTTCCC 59.738 38.462 0.00 0.00 0.00 3.97
1871 1902 7.259290 TGCGTTTTCTATTCCTATGATTTCC 57.741 36.000 0.00 0.00 0.00 3.13
1872 1903 9.387123 GAATGCGTTTTCTATTCCTATGATTTC 57.613 33.333 0.00 0.00 0.00 2.17
1873 1904 9.125026 AGAATGCGTTTTCTATTCCTATGATTT 57.875 29.630 0.00 0.00 34.21 2.17
1874 1905 8.562892 CAGAATGCGTTTTCTATTCCTATGATT 58.437 33.333 0.00 0.00 34.21 2.57
1875 1906 7.933577 TCAGAATGCGTTTTCTATTCCTATGAT 59.066 33.333 0.00 0.00 34.21 2.45
1876 1907 7.272244 TCAGAATGCGTTTTCTATTCCTATGA 58.728 34.615 0.00 0.00 34.21 2.15
1877 1908 7.307632 CCTCAGAATGCGTTTTCTATTCCTATG 60.308 40.741 0.00 0.00 34.21 2.23
1878 1909 6.708054 CCTCAGAATGCGTTTTCTATTCCTAT 59.292 38.462 0.00 0.00 34.21 2.57
1879 1910 6.049149 CCTCAGAATGCGTTTTCTATTCCTA 58.951 40.000 0.00 0.00 34.21 2.94
1880 1911 4.878397 CCTCAGAATGCGTTTTCTATTCCT 59.122 41.667 0.00 0.00 34.21 3.36
1881 1912 4.636206 ACCTCAGAATGCGTTTTCTATTCC 59.364 41.667 0.00 0.00 34.21 3.01
1882 1913 5.803020 ACCTCAGAATGCGTTTTCTATTC 57.197 39.130 0.00 0.00 34.21 1.75
1883 1914 5.585047 GGTACCTCAGAATGCGTTTTCTATT 59.415 40.000 4.06 0.00 34.21 1.73
1884 1915 5.116882 GGTACCTCAGAATGCGTTTTCTAT 58.883 41.667 4.06 0.00 34.21 1.98
1885 1916 4.020928 TGGTACCTCAGAATGCGTTTTCTA 60.021 41.667 14.36 0.00 34.21 2.10
1886 1917 3.244422 TGGTACCTCAGAATGCGTTTTCT 60.244 43.478 14.36 0.00 36.38 2.52
1887 1918 3.071479 TGGTACCTCAGAATGCGTTTTC 58.929 45.455 14.36 0.00 34.76 2.29
1888 1919 3.134574 TGGTACCTCAGAATGCGTTTT 57.865 42.857 14.36 0.00 34.76 2.43
1889 1920 2.851263 TGGTACCTCAGAATGCGTTT 57.149 45.000 14.36 0.00 34.76 3.60
1890 1921 3.009723 CAATGGTACCTCAGAATGCGTT 58.990 45.455 14.36 0.00 34.76 4.84
1936 1967 4.942761 TGACTTTAAGTGGTACCTTCGT 57.057 40.909 14.36 7.33 0.00 3.85
2017 2048 0.759959 TTACTTCCCGACCAGTTGCA 59.240 50.000 0.00 0.00 0.00 4.08
2320 2351 1.814394 ACACCACGTATGAAGCGAGTA 59.186 47.619 6.02 0.00 0.00 2.59
2342 2373 0.169672 GTACTCCGCTCGTTGTAGCA 59.830 55.000 0.00 0.00 42.91 3.49
2445 2476 1.305297 AGATGGTGGACTGAGCCGA 60.305 57.895 0.00 0.00 0.00 5.54
2452 2483 2.248248 TGTCGAAAGAGATGGTGGACT 58.752 47.619 0.00 0.00 43.49 3.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.